PRJNA658001 HISAT2 Samtools Flagstat MultiQC: MultiQC Report

PRJNA658001 HISAT2 Samtools Flagstat MultiQC

A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

Report generated on 2025-11-16, 00:50 CET based on data in: /data/jwd06/main/091/834/91834135/working/multiqc_WDir

General Statistics

Showing ¹⁴⁴/₁₄₄ rows and ¹/₃ columns.

Sample Name	Reads	Reads mapped	% Reads mapped
SRR12475103	39.9M	38.3M	96.0%
SRR12475104	25.9M	24.5M	94.5%
SRR12475105	24.3M	23.3M	95.8%
SRR12475106	28.5M	27.9M	97.7%
SRR12475107	32.3M	31.5M	97.7%
SRR12475108	40.3M	39.1M	97.0%
SRR12475109	47.9M	46.8M	97.7%
SRR12475110	59.6M	58.2M	97.6%
SRR12475111	52.6M	51.1M	97.0%
SRR12475112	80.3M	78.2M	97.3%
SRR12475113	64.8M	63.4M	97.8%
SRR12475114	99.4M	96.7M	97.3%
SRR12475115	59.8M	58.0M	97.0%
SRR12475116	81.6M	79.6M	97.6%
SRR12475117	62.1M	60.7M	97.7%
SRR12475118	59.7M	58.3M	97.7%
SRR12475119	66.1M	64.1M	97.0%
SRR12475120	64.4M	62.9M	97.7%
SRR12475121	59.2M	57.8M	97.6%
SRR12475122	66.8M	65.1M	97.5%
SRR12475123	43.9M	42.7M	97.5%
SRR12475124	10.6M	9.7M	91.0%
SRR12475125	35.4M	34.6M	97.7%
SRR12475126	41.5M	40.5M	97.7%
SRR12475127	14.3M	13.5M	94.3%
SRR12475128	43.9M	42.9M	97.8%
SRR12475129	78.6M	76.6M	97.5%
SRR12475130	48.0M	46.9M	97.5%
SRR12475131	62.2M	60.6M	97.4%
SRR12475132	71.3M	69.5M	97.5%
SRR12475133	68.6M	67.0M	97.6%
SRR12475134	63.5M	61.5M	96.9%
SRR12475135	59.7M	58.3M	97.7%
SRR12475136	63.6M	62.1M	97.6%
SRR12475137	57.6M	56.2M	97.6%
SRR12475138	69.9M	68.2M	97.6%
SRR12475139	47.4M	46.3M	97.5%
SRR12475140	48.9M	47.6M	97.5%
SRR12475141	25.1M	23.8M	94.8%
SRR12475142	16.2M	15.8M	97.6%
SRR12475143	28.3M	27.5M	97.3%
SRR12475144	49.2M	48.2M	97.9%
SRR12475145	17.3M	16.8M	97.0%
SRR12475146	19.7M	19.1M	97.1%
SRR12475147	48.2M	47.1M	97.7%
SRR12475148	40.1M	39.2M	97.7%
SRR12475149	60.5M	59.1M	97.7%
SRR12475150	50.9M	49.7M	97.7%
SRR12475151	33.0M	31.8M	96.5%
SRR12475152	28.8M	27.7M	96.2%
SRR12475153	15.0M	13.8M	92.5%
SRR12475154	26.1M	24.8M	95.2%
SRR12475155	9.1M	8.2M	90.5%
SRR12475156	16.1M	15.2M	94.1%
SRR12475157	9.6M	8.8M	91.9%
SRR12475158	27.1M	25.8M	95.2%
SRR12475159	41.6M	40.1M	96.5%
SRR12475160	37.0M	35.6M	96.2%
SRR12475161	48.7M	47.0M	96.5%
SRR12475162	41.3M	39.7M	96.2%
SRR12475163	38.5M	37.3M	96.9%
SRR12475164	32.9M	31.8M	96.8%
SRR12475165	60.5M	58.3M	96.4%
SRR12475166	54.8M	53.2M	97.1%
SRR12475167	50.5M	48.8M	96.7%
SRR12475168	43.5M	41.9M	96.4%
SRR12475169	39.7M	38.4M	96.8%
SRR12475170	45.3M	43.6M	96.2%
SRR12475171	41.1M	39.7M	96.6%
SRR12475172	21.3M	20.2M	95.0%
SRR12475173	38.5M	37.1M	96.4%
SRR12475174	34.3M	32.5M	94.6%
SRR12475175	37.3M	36.1M	96.7%
SRR12475176	37.4M	35.7M	95.5%
SRR12475177	41.2M	40.1M	97.2%
SRR12475178	40.6M	39.3M	96.8%
SRR12475179	46.2M	44.9M	97.3%
SRR12475180	36.8M	35.3M	96.1%
SRR12475181	52.3M	51.0M	97.6%
SRR12475182	41.4M	40.1M	96.8%
SRR12475183	35.6M	34.2M	96.1%
SRR12475184	71.8M	70.0M	97.5%
SRR12475185	68.6M	66.7M	97.3%
SRR12475186	63.0M	61.2M	97.3%
SRR12475187	57.6M	55.8M	97.0%
SRR12475188	62.9M	61.3M	97.4%
SRR12475189	41.2M	39.7M	96.5%
SRR12475190	43.7M	42.5M	97.1%
SRR12475191	37.6M	35.4M	94.2%
SRR12475192	26.3M	25.6M	97.2%
SRR12475193	42.3M	41.2M	97.5%
SRR12475194	31.4M	30.5M	97.4%
SRR12475195	41.5M	40.1M	96.7%
SRR12475196	50.0M	48.3M	96.6%
SRR12475197	50.8M	49.5M	97.3%
SRR12475198	34.4M	33.5M	97.2%
SRR12475199	37.6M	36.4M	97.0%
SRR12475200	49.6M	48.3M	97.4%
SRR12475201	73.5M	71.7M	97.5%
SRR12475202	33.8M	32.9M	97.4%
SRR12475203	48.1M	46.4M	96.6%
SRR12475204	31.4M	30.5M	97.1%
SRR12475205	35.7M	34.7M	97.2%
SRR12475206	48.8M	47.5M	97.3%
SRR12475207	39.8M	38.8M	97.4%
SRR12475208	43.7M	42.6M	97.5%
SRR12475209	40.2M	39.1M	97.2%
SRR12475210	35.2M	34.0M	96.6%
SRR12475211	30.5M	29.7M	97.4%
SRR12475212	43.1M	42.1M	97.6%
SRR12475213	29.0M	28.2M	97.1%
SRR12475214	31.8M	30.6M	96.2%
SRR12475215	46.2M	44.8M	96.9%
SRR12475216	33.0M	32.2M	97.4%
SRR12475217	38.2M	37.2M	97.4%
SRR12475218	33.7M	32.9M	97.6%
SRR12475219	53.0M	51.5M	97.2%
SRR12475220	51.8M	50.4M	97.3%
SRR12475221	60.4M	58.8M	97.4%
SRR12475222	51.8M	50.4M	97.4%
SRR12475223	37.1M	35.6M	95.9%
SRR12475224	34.7M	33.4M	96.2%
SRR12475225	28.3M	26.9M	95.2%
SRR12475226	25.0M	23.8M	95.0%
SRR12475227	26.4M	25.2M	95.4%
SRR12475228	21.2M	20.0M	94.7%
SRR12475229	34.0M	32.1M	94.4%
SRR12475230	29.6M	28.2M	95.3%
SRR12475231	44.5M	43.0M	96.4%
SRR12475232	38.4M	37.0M	96.4%
SRR12475233	44.6M	42.8M	95.9%
SRR12475234	39.1M	37.4M	95.7%
SRR12475235	29.9M	28.9M	96.4%
SRR12475236	22.8M	21.8M	95.8%
SRR12475237	47.6M	45.4M	95.5%
SRR12475238	48.0M	46.0M	95.9%
SRR12475239	42.0M	40.0M	95.2%
SRR12475240	38.8M	37.3M	95.9%
SRR12475241	37.7M	36.1M	96.0%
SRR12475242	38.4M	36.8M	95.8%
SRR12475243	36.6M	35.0M	95.6%
SRR12475244	27.0M	25.7M	95.1%
SRR12475245	37.7M	36.3M	96.1%
SRR12475246	33.1M	31.8M	96.2%

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: general_stats_table_table

Sort	Group	Column	Description	ID	Scale
\|\|	Samtools: flagstat	Reads	Total reads in the bam file (millions)	`samtools_flagstat-flagstat_total`	read_count
\|\|	Samtools: flagstat	Reads mapped	Reads mapped in the bam file (millions)	`samtools_flagstat-mapped_passed`	read_count
\|\|	Samtools: flagstat	% Reads mapped	% Reads mapped in the bam file	`samtools_flagstat-mapped_passed_pct`

Showing ¹⁴⁴/₁₄₄ rows and ¹¹/₁₁ columns.

Sample Name	Total Reads	Total Passed QC	Mapped	Secondary Alignments	Duplicates	Paired in Sequencing	Properly Paired	Self and mate mapped	Singletons	Mate mapped to diff chr	Diff chr (mapQ >= 5)
SRR12475103	39.9M	39.9M	38.3M	5.0M	0.0M	34.9M	32.1M	33.0M	0.3M	0.4M	0.4M
SRR12475104	25.9M	25.9M	24.5M	3.9M	0.0M	22.0M	20.0M	20.3M	0.2M	0.1M	0.1M
SRR12475105	24.3M	24.3M	23.3M	3.6M	0.0M	20.7M	19.0M	19.5M	0.2M	0.2M	0.1M
SRR12475106	28.5M	28.5M	27.9M	8.0M	0.0M	20.6M	19.4M	19.7M	0.2M	0.1M	0.1M
SRR12475107	32.3M	32.3M	31.5M	4.8M	0.0M	27.5M	26.1M	26.5M	0.3M	0.1M	0.1M
SRR12475108	40.3M	40.3M	39.1M	6.1M	0.0M	34.2M	31.8M	32.5M	0.5M	0.3M	0.3M
SRR12475109	47.9M	47.9M	46.8M	6.2M	0.0M	41.7M	39.4M	40.0M	0.6M	0.2M	0.1M
SRR12475110	59.6M	59.6M	58.2M	8.1M	0.0M	51.5M	48.6M	49.4M	0.6M	0.4M	0.3M
SRR12475111	52.6M	52.6M	51.1M	7.0M	0.0M	45.6M	42.8M	43.4M	0.6M	0.2M	0.1M
SRR12475112	80.3M	80.3M	78.2M	11.3M	0.0M	69.0M	65.1M	66.0M	0.9M	0.4M	0.3M
SRR12475113	64.8M	64.8M	63.4M	8.2M	0.0M	56.6M	53.8M	54.5M	0.7M	0.3M	0.3M
SRR12475114	99.4M	99.4M	96.7M	13.1M	0.0M	86.3M	81.3M	82.4M	1.2M	0.6M	0.4M
SRR12475115	59.8M	59.8M	58.0M	8.1M	0.0M	51.7M	48.5M	49.2M	0.8M	0.4M	0.3M
SRR12475116	81.6M	81.6M	79.6M	9.5M	0.0M	72.1M	68.5M	69.3M	0.8M	0.4M	0.3M
SRR12475117	62.1M	62.1M	60.7M	7.7M	0.0M	54.4M	51.7M	52.3M	0.7M	0.3M	0.3M
SRR12475118	59.7M	59.7M	58.3M	7.4M	0.0M	52.2M	49.2M	50.1M	0.7M	0.4M	0.4M
SRR12475119	66.1M	66.1M	64.1M	9.2M	0.0M	56.9M	53.3M	54.1M	0.9M	0.4M	0.3M
SRR12475120	64.4M	64.4M	62.9M	8.2M	0.0M	56.2M	53.3M	54.1M	0.6M	0.3M	0.3M
SRR12475121	59.2M	59.2M	57.8M	7.7M	0.0M	51.5M	48.5M	49.4M	0.7M	0.4M	0.4M
SRR12475122	66.8M	66.8M	65.1M	8.7M	0.0M	58.1M	54.9M	55.7M	0.8M	0.4M	0.4M
SRR12475123	43.9M	43.9M	42.7M	10.2M	0.0M	33.7M	31.5M	32.0M	0.5M	0.2M	0.2M
SRR12475124	10.6M	10.6M	9.7M	2.0M	0.0M	8.6M	6.8M	7.3M	0.3M	0.2M	0.1M
SRR12475125	35.4M	35.4M	34.6M	4.9M	0.0M	30.5M	28.9M	29.3M	0.4M	0.1M	0.1M
SRR12475126	41.5M	41.5M	40.5M	5.7M	0.0M	35.7M	34.0M	34.4M	0.4M	0.1M	0.1M
SRR12475127	14.3M	14.3M	13.5M	2.2M	0.0M	12.1M	10.5M	10.9M	0.4M	0.1M	0.0M
SRR12475128	43.9M	43.9M	42.9M	6.0M	0.0M	37.9M	36.1M	36.5M	0.4M	0.2M	0.1M
SRR12475129	78.6M	78.6M	76.6M	11.3M	0.0M	67.2M	63.5M	64.3M	0.9M	0.4M	0.3M
SRR12475130	48.0M	48.0M	46.9M	6.7M	0.0M	41.4M	39.1M	39.6M	0.5M	0.3M	0.2M
SRR12475131	62.2M	62.2M	60.6M	8.5M	0.0M	53.7M	50.4M	51.4M	0.8M	0.4M	0.3M
SRR12475132	71.3M	71.3M	69.5M	8.9M	0.0M	62.4M	59.0M	59.8M	0.8M	0.4M	0.3M
SRR12475133	68.6M	68.6M	67.0M	9.7M	0.0M	58.9M	55.9M	56.6M	0.7M	0.3M	0.3M
SRR12475134	63.5M	63.5M	61.5M	9.1M	0.0M	54.4M	50.9M	51.6M	0.8M	0.3M	0.2M
SRR12475135	59.7M	59.7M	58.3M	8.4M	0.0M	51.3M	48.7M	49.3M	0.6M	0.3M	0.2M
SRR12475136	63.6M	63.6M	62.1M	9.6M	0.0M	54.0M	51.0M	51.9M	0.6M	0.4M	0.3M
SRR12475137	57.6M	57.6M	56.2M	6.8M	0.0M	50.8M	48.2M	48.8M	0.6M	0.3M	0.3M
SRR12475138	69.9M	69.9M	68.2M	8.9M	0.0M	61.0M	58.1M	58.6M	0.7M	0.3M	0.2M
SRR12475139	47.4M	47.4M	46.3M	6.7M	0.0M	40.7M	38.3M	39.0M	0.5M	0.3M	0.2M
SRR12475140	48.9M	48.9M	47.6M	6.3M	0.0M	42.5M	40.2M	40.7M	0.5M	0.2M	0.1M
SRR12475141	25.1M	25.1M	23.8M	4.2M	0.0M	20.9M	19.0M	19.3M	0.3M	0.1M	0.1M
SRR12475142	16.2M	16.2M	15.8M	2.3M	0.0M	13.8M	13.1M	13.3M	0.2M	0.1M	0.1M
SRR12475143	28.3M	28.3M	27.5M	4.5M	0.0M	23.8M	22.4M	22.7M	0.3M	0.1M	0.1M
SRR12475144	49.2M	49.2M	48.2M	7.3M	0.0M	42.0M	40.1M	40.4M	0.5M	0.2M	0.1M
SRR12475145	17.3M	17.3M	16.8M	3.2M	0.0M	14.1M	13.0M	13.4M	0.2M	0.1M	0.1M
SRR12475146	19.7M	19.7M	19.1M	3.5M	0.0M	16.2M	15.1M	15.4M	0.2M	0.1M	0.1M
SRR12475147	48.2M	48.2M	47.1M	6.4M	0.0M	41.8M	39.3M	40.1M	0.5M	0.3M	0.3M
SRR12475148	40.1M	40.1M	39.2M	7.7M	0.0M	32.5M	30.4M	31.1M	0.4M	0.3M	0.2M
SRR12475149	60.5M	60.5M	59.1M	9.2M	0.0M	51.3M	48.6M	49.2M	0.7M	0.3M	0.2M
SRR12475150	50.9M	50.9M	49.7M	6.8M	0.0M	44.1M	41.8M	42.4M	0.6M	0.3M	0.2M
SRR12475151	33.0M	33.0M	31.8M	5.0M	0.0M	27.9M	25.6M	26.4M	0.4M	0.1M	0.1M
SRR12475152	28.8M	28.8M	27.7M	4.7M	0.0M	24.1M	21.8M	22.6M	0.3M	0.1M	0.1M
SRR12475153	15.0M	15.0M	13.8M	2.6M	0.0M	12.4M	10.3M	11.0M	0.3M	0.1M	0.1M
SRR12475154	26.1M	26.1M	24.8M	4.7M	0.0M	21.4M	18.9M	19.8M	0.4M	0.1M	0.1M
SRR12475155	9.1M	9.1M	8.2M	1.6M	0.0M	7.4M	5.7M	6.3M	0.3M	0.1M	0.1M
SRR12475156	16.1M	16.1M	15.2M	2.7M	0.0M	13.4M	11.5M	12.2M	0.3M	0.1M	0.1M
SRR12475157	9.6M	9.6M	8.8M	1.4M	0.0M	8.2M	6.5M	7.1M	0.3M	0.1M	0.1M
SRR12475158	27.1M	27.1M	25.8M	4.4M	0.0M	22.7M	20.1M	21.0M	0.4M	0.1M	0.1M
SRR12475159	41.6M	41.6M	40.1M	6.9M	0.0M	34.7M	31.8M	32.8M	0.4M	0.1M	0.1M
SRR12475160	37.0M	37.0M	35.6M	5.8M	0.0M	31.2M	28.4M	29.4M	0.4M	0.1M	0.1M
SRR12475161	48.7M	48.7M	47.0M	7.5M	0.0M	41.2M	37.9M	39.0M	0.5M	0.1M	0.1M
SRR12475162	41.3M	41.3M	39.7M	7.0M	0.0M	34.2M	31.3M	32.3M	0.4M	0.1M	0.1M
SRR12475163	38.5M	38.5M	37.3M	5.8M	0.0M	32.7M	30.3M	31.2M	0.3M	0.1M	0.1M
SRR12475164	32.9M	32.9M	31.8M	5.5M	0.0M	27.3M	25.2M	26.0M	0.3M	0.1M	0.0M
SRR12475165	60.5M	60.5M	58.3M	11.5M	0.0M	49.1M	45.2M	46.5M	0.4M	0.1M	0.0M
SRR12475166	54.8M	54.8M	53.2M	10.3M	0.0M	44.5M	41.4M	42.6M	0.3M	0.1M	0.0M
SRR12475167	50.5M	50.5M	48.8M	8.7M	0.0M	41.7M	38.6M	39.7M	0.4M	0.1M	0.0M
SRR12475168	43.5M	43.5M	41.9M	7.5M	0.0M	36.0M	33.1M	34.1M	0.4M	0.1M	0.0M
SRR12475169	39.7M	39.7M	38.4M	6.9M	0.0M	32.8M	30.3M	31.2M	0.3M	0.1M	0.0M
SRR12475170	45.3M	45.3M	43.6M	7.0M	0.0M	38.3M	35.1M	36.2M	0.4M	0.1M	0.0M
SRR12475171	41.1M	41.1M	39.7M	7.6M	0.0M	33.5M	30.8M	31.7M	0.3M	0.1M	0.0M
SRR12475172	21.3M	21.3M	20.2M	5.6M	0.0M	15.6M	13.9M	14.4M	0.1M	0.1M	0.0M
SRR12475173	38.5M	38.5M	37.1M	7.0M	0.0M	31.4M	28.9M	29.8M	0.3M	0.1M	0.0M
SRR12475174	34.3M	34.3M	32.5M	6.2M	0.0M	28.2M	25.1M	26.0M	0.3M	0.1M	0.0M
SRR12475175	37.3M	37.3M	36.1M	4.4M	0.0M	33.0M	30.6M	31.3M	0.5M	0.2M	0.2M
SRR12475176	37.4M	37.4M	35.7M	3.8M	0.0M	33.6M	30.8M	31.5M	0.4M	0.2M	0.2M
SRR12475177	41.2M	41.2M	40.1M	5.0M	0.0M	36.2M	33.9M	34.5M	0.5M	0.2M	0.1M
SRR12475178	40.6M	40.6M	39.3M	4.9M	0.0M	35.7M	33.0M	33.8M	0.6M	0.2M	0.1M
SRR12475179	46.2M	46.2M	44.9M	5.8M	0.0M	40.3M	37.8M	38.5M	0.6M	0.2M	0.2M
SRR12475180	36.8M	36.8M	35.3M	4.0M	0.0M	32.8M	30.3M	30.9M	0.4M	0.2M	0.2M
SRR12475181	52.3M	52.3M	51.0M	6.5M	0.0M	45.7M	43.3M	43.9M	0.6M	0.3M	0.2M
SRR12475182	41.4M	41.4M	40.1M	5.4M	0.0M	36.0M	33.5M	34.2M	0.5M	0.3M	0.2M
SRR12475183	35.6M	35.6M	34.2M	4.4M	0.0M	31.2M	28.5M	29.3M	0.5M	0.3M	0.2M
SRR12475184	71.8M	71.8M	70.0M	9.5M	0.0M	62.4M	58.8M	59.7M	0.8M	0.4M	0.3M
SRR12475185	68.6M	68.6M	66.7M	8.9M	0.0M	59.6M	56.0M	56.9M	0.9M	0.4M	0.3M
SRR12475186	63.0M	63.0M	61.2M	8.1M	0.0M	54.8M	51.3M	52.3M	0.8M	0.4M	0.3M
SRR12475187	57.6M	57.6M	55.8M	7.9M	0.0M	49.7M	46.5M	47.2M	0.7M	0.3M	0.2M
SRR12475188	62.9M	62.9M	61.3M	8.0M	0.0M	54.9M	51.9M	52.6M	0.7M	0.4M	0.3M
SRR12475189	41.2M	41.2M	39.7M	5.7M	0.0M	35.5M	33.0M	33.5M	0.5M	0.2M	0.2M
SRR12475190	43.7M	43.7M	42.5M	6.4M	0.0M	37.3M	35.1M	35.6M	0.5M	0.2M	0.2M
SRR12475191	37.6M	37.6M	35.4M	5.5M	0.0M	32.1M	28.9M	29.4M	0.5M	0.2M	0.2M
SRR12475192	26.3M	26.3M	25.6M	3.9M	0.0M	22.4M	21.0M	21.3M	0.3M	0.1M	0.1M
SRR12475193	42.3M	42.3M	41.2M	6.2M	0.0M	36.1M	34.0M	34.6M	0.5M	0.2M	0.2M
SRR12475194	31.4M	31.4M	30.5M	5.0M	0.0M	26.4M	24.8M	25.2M	0.4M	0.2M	0.1M
SRR12475195	41.5M	41.5M	40.1M	7.4M	0.0M	34.1M	31.6M	32.1M	0.6M	0.2M	0.1M
SRR12475196	50.0M	50.0M	48.3M	7.7M	0.0M	42.3M	39.2M	39.9M	0.7M	0.3M	0.2M
SRR12475197	50.8M	50.8M	49.5M	7.5M	0.0M	43.4M	40.7M	41.3M	0.6M	0.2M	0.1M
SRR12475198	34.4M	34.4M	33.5M	5.4M	0.0M	29.0M	27.1M	27.6M	0.5M	0.2M	0.1M
SRR12475199	37.6M	37.6M	36.4M	6.2M	0.0M	31.3M	29.2M	29.7M	0.5M	0.2M	0.1M
SRR12475200	49.6M	49.6M	48.3M	7.4M	0.0M	42.1M	39.7M	40.2M	0.6M	0.2M	0.2M
SRR12475201	73.5M	73.5M	71.7M	10.4M	0.0M	63.1M	59.7M	60.5M	0.8M	0.4M	0.3M
SRR12475202	33.8M	33.8M	32.9M	5.1M	0.0M	28.7M	27.1M	27.5M	0.4M	0.2M	0.1M
SRR12475203	48.1M	48.1M	46.4M	7.6M	0.0M	40.4M	37.6M	38.1M	0.7M	0.2M	0.2M
SRR12475204	31.4M	31.4M	30.5M	4.5M	0.0M	26.9M	25.1M	25.6M	0.4M	0.1M	0.1M
SRR12475205	35.7M	35.7M	34.7M	5.5M	0.0M	30.3M	28.4M	28.8M	0.4M	0.2M	0.1M
SRR12475206	48.8M	48.8M	47.5M	7.4M	0.0M	41.5M	39.0M	39.6M	0.6M	0.2M	0.2M
SRR12475207	39.8M	39.8M	38.8M	5.5M	0.0M	34.3M	32.2M	32.8M	0.5M	0.2M	0.2M
SRR12475208	43.7M	43.7M	42.6M	6.4M	0.0M	37.3M	35.1M	35.6M	0.5M	0.2M	0.2M
SRR12475209	40.2M	40.2M	39.1M	6.1M	0.0M	34.1M	32.0M	32.5M	0.5M	0.2M	0.1M
SRR12475210	35.2M	35.2M	34.0M	5.9M	0.0M	29.3M	27.3M	27.7M	0.4M	0.1M	0.1M
SRR12475211	30.5M	30.5M	29.7M	4.7M	0.0M	25.8M	24.2M	24.7M	0.4M	0.2M	0.1M
SRR12475212	43.1M	43.1M	42.1M	6.2M	0.0M	37.0M	35.1M	35.5M	0.4M	0.2M	0.1M
SRR12475213	29.0M	29.0M	28.2M	5.2M	0.0M	23.8M	22.1M	22.6M	0.4M	0.2M	0.1M
SRR12475214	31.8M	31.8M	30.6M	5.1M	0.0M	26.7M	24.5M	25.1M	0.5M	0.2M	0.1M
SRR12475215	46.2M	46.2M	44.8M	7.1M	0.0M	39.2M	36.6M	37.1M	0.6M	0.2M	0.2M
SRR12475216	33.0M	33.0M	32.2M	5.4M	0.0M	27.6M	26.0M	26.4M	0.4M	0.2M	0.1M
SRR12475217	38.2M	38.2M	37.2M	5.7M	0.0M	32.5M	30.5M	31.0M	0.5M	0.2M	0.2M
SRR12475218	33.7M	33.7M	32.9M	5.4M	0.0M	28.3M	26.5M	27.1M	0.4M	0.3M	0.2M
SRR12475219	53.0M	53.0M	51.5M	7.4M	0.0M	45.7M	42.3M	43.4M	0.8M	0.4M	0.3M
SRR12475220	51.8M	51.8M	50.4M	8.8M	0.0M	42.9M	39.8M	40.9M	0.6M	0.4M	0.3M
SRR12475221	60.4M	60.4M	58.8M	8.2M	0.0M	52.2M	49.0M	49.9M	0.7M	0.3M	0.2M
SRR12475222	51.8M	51.8M	50.4M	6.3M	0.0M	45.5M	42.7M	43.5M	0.7M	0.3M	0.2M
SRR12475223	37.1M	37.1M	35.6M	5.0M	0.0M	32.2M	29.3M	30.2M	0.4M	0.1M	0.1M
SRR12475224	34.7M	34.7M	33.4M	4.9M	0.0M	29.9M	27.2M	28.1M	0.4M	0.1M	0.1M
SRR12475225	28.3M	28.3M	26.9M	4.5M	0.0M	23.7M	21.2M	22.0M	0.4M	0.1M	0.1M
SRR12475226	25.0M	25.0M	23.8M	3.7M	0.0M	21.3M	18.9M	19.7M	0.4M	0.1M	0.1M
SRR12475227	26.4M	26.4M	25.2M	4.3M	0.0M	22.1M	19.7M	20.5M	0.4M	0.1M	0.1M
SRR12475228	21.2M	21.2M	20.0M	3.9M	0.0M	17.2M	15.0M	15.8M	0.3M	0.1M	0.1M
SRR12475229	34.0M	34.0M	32.1M	6.1M	0.0M	27.9M	24.5M	25.5M	0.5M	0.1M	0.1M
SRR12475230	29.6M	29.6M	28.2M	4.6M	0.0M	25.0M	22.3M	23.2M	0.4M	0.2M	0.1M
SRR12475231	44.5M	44.5M	43.0M	7.0M	0.0M	37.5M	34.4M	35.5M	0.5M	0.2M	0.1M
SRR12475232	38.4M	38.4M	37.0M	5.5M	0.0M	32.9M	30.1M	31.1M	0.4M	0.1M	0.1M
SRR12475233	44.6M	44.6M	42.8M	6.7M	0.0M	37.8M	34.5M	35.5M	0.5M	0.2M	0.1M
SRR12475234	39.1M	39.1M	37.4M	6.4M	0.0M	32.7M	29.6M	30.6M	0.4M	0.1M	0.1M
SRR12475235	29.9M	29.9M	28.9M	4.3M	0.0M	25.6M	23.5M	24.2M	0.3M	0.1M	0.1M
SRR12475236	22.8M	22.8M	21.8M	3.9M	0.0M	18.9M	17.0M	17.6M	0.3M	0.1M	0.0M
SRR12475237	47.6M	47.6M	45.4M	8.5M	0.0M	39.0M	35.5M	36.5M	0.4M	0.1M	0.0M
SRR12475238	48.0M	48.0M	46.0M	8.6M	0.0M	39.4M	36.1M	37.1M	0.3M	0.1M	0.0M
SRR12475239	42.0M	42.0M	40.0M	7.5M	0.0M	34.5M	31.3M	32.1M	0.4M	0.1M	0.0M
SRR12475240	38.8M	38.8M	37.3M	6.5M	0.0M	32.4M	29.6M	30.5M	0.3M	0.1M	0.0M
SRR12475241	37.7M	37.7M	36.1M	6.4M	0.0M	31.3M	28.5M	29.4M	0.3M	0.1M	0.0M
SRR12475242	38.4M	38.4M	36.8M	6.2M	0.0M	32.2M	29.3M	30.2M	0.4M	0.1M	0.0M
SRR12475243	36.6M	36.6M	35.0M	6.4M	0.0M	30.2M	27.4M	28.2M	0.4M	0.1M	0.0M
SRR12475244	27.0M	27.0M	25.7M	6.1M	0.0M	20.9M	18.7M	19.3M	0.3M	0.1M	0.0M
SRR12475245	37.7M	37.7M	36.3M	6.6M	0.0M	31.1M	28.5M	29.3M	0.3M	0.1M	0.0M
SRR12475246	33.1M	33.1M	31.8M	6.3M	0.0M	26.8M	24.5M	25.3M	0.3M	0.1M	0.0M

v1.27

PRJNA658001 HISAT2 Samtools Flagstat MultiQC

MultiQC Toolbox

Highlight Samples

Rename Samples

Show / Hide Samples

Explain with AI

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

PRJNA658001 HISAT2 Samtools Flagstat MultiQC

General Statistics

Samtools

Flagstat

Sort	Column	Description	ID	Scale
\|\|	Total Reads	Total Reads	`flagstat_total`	read_count
\|\|	Total Passed QC	Total Passed QC	`total_passed`	read_count
\|\|	Mapped	Mapped	`mapped_passed`	read_count
\|\|	Secondary Alignments	Secondary Alignments	`secondary_passed`	read_count
\|\|	Duplicates	Duplicates	`duplicates_passed`	read_count
\|\|	Paired in Sequencing	Paired in Sequencing	`paired_in_sequencing_passed`	read_count
\|\|	Properly Paired	Properly Paired	`properly_paired_passed`	read_count
\|\|	Self and mate mapped	Reads with itself and mate mapped	`with_itself_and_mate_mapped_passed`	read_count
\|\|	Singletons	Singletons	`singletons_passed`	read_count
\|\|	Mate mapped to diff chr	Mate mapped to different chromosome	`with_mate_mapped_to_a_different_chr_passed`	read_count
\|\|	Diff chr (mapQ >= 5)	Mate mapped to different chromosome (mapQ >= 5)	`with_mate_mapped_to_a_different_chr_mapQ_5__passed`	read_count

Toggle navigation v1.27

PRJNA658001 HISAT2 Samtools Flagstat MultiQC

MultiQC Toolbox

Apply Highlight Samples

Apply Rename Samples

Apply Show / Hide Samples

Explain with AI

Export Plots

Choose Plots

Save Settings

Load Settings

Tool Citations

About MultiQC

PRJNA658001 HISAT2 Samtools Flagstat MultiQC

General Statistics

General Statistics: Columns

Samtools

Flagstat

Samtools: flagstat: read count: Columns

v1.27

Highlight Samples

Rename Samples

Show / Hide Samples